Etool - Genome Assemblyhttp://etool.me/news/topic/1000000014/Genome-Assembly
Genome AssemblyThu, 17 Aug 2017 22:06:26 GMTCopyright: (C) Etool.Me Group, see http://etool.me/terms-of-use for terms and conditions of reuse.15QUAST: quality assessment tool for genome assemblies Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics.http://etool.me/news/90000000008/QUAST:-quality-assessment-tool-for-genome-assemblies
Thu, 26 Sep 2013 07:30:44 GMTIDBA-UD: A single cell assembler. IDBA-UD: an algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. http://etool.me/news/90000000007/IDBA-UD:-A-single-cell-assembler.-
Thu, 26 Sep 2013 07:30:58 GMTC-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparisonWe present Comparative Sibelia software (C-Sibelia) for the comparison of two bacterial genomes in the form of complete sequences or draft assemblies. C-Sibelia is able to compare genomes in the presence of rearrangements and duplications. C-Sibelia takes as input two FASTA files (the assembly and reference files; if the reference genome is not available, it can be substituted by another draft assembly) and produces: (1) a VCF file containing all identified single nucleotide variations (SNVs) and indels; (2) annotation of these variants by SnpEff; (3) an XMFA1 file containing alignment information. The web-based version also produces a circular diagram visualizing the rearrangement of synteny blocks in two genomes.http://etool.me/news/90000000020/C-Sibelia:-an-easy-to-use-and-highly-accurate-tool-for-bacterial-genome-comparison
Mon, 25 Nov 2013 17:58:11 GMTDe novo genome assembly: what every biologist should knowAsked how mature the field of genome assembly is, Ian Korf at the University of California, Davis, compares it to a teenager with great capabilities. “It's got bold assertions about what it can do, but at the same time it's making embarrassing mistakes,” he says. Perhaps the biggest barrier to maturity is that there are few ways to distinguish true insight from foolish gaffe. When a species' genome is newly assembled, no one knows what's real, what's missing, and what's experimental artifact.http://etool.me/news/90000000034/De-novo-genome-assembly:-what-every-biologist-should-know
Thu, 27 Feb 2014 15:24:38 GMTSPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly.http://etool.me/news/90000000006/SPAdes:-A-New-Genome-Assembly-Algorithm-and-Its-Applications-to-Single-Cell-Sequencing
Thu, 26 Sep 2013 07:31:09 GMTFrom Indexing Data Structures to de Bruijn GraphsNew technologies have tremendously increased sequencing throughput compared to traditional techniques, thereby complicating DNA assembly.http://etool.me/news/90000000047/From-Indexing-Data-Structures-to-de-Bruijn-Graphs
Fri, 31 Oct 2014 22:03:42 GMT